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- PDB-6imu: The apo-structure of endo-beta-1,2-glucanase from Talaromyces fun... -

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Basic information

Entry
Database: PDB / ID: 6imu
TitleThe apo-structure of endo-beta-1,2-glucanase from Talaromyces funiculosus
ComponentsEndo-beta-1,2-glucanase
KeywordsHYDROLASE / Glycoside hydrolase / Talaromyces funiculosus
Function / homologyglucan endo-1,2-beta-glucosidase / glucan endo-1,2-beta-glucosidase activity / CITRIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Endo-beta-1,2-glucanase
Function and homology information
Biological speciesTalaromyces funiculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTanaka, N. / Nakajima, M. / Narukawa-Nara, M. / Matsunaga, H. / Kamisuki, S. / Aramasa, H. / Takahashi, Y. / Sugimoto, N. / Abe, K. / Miyanaga, A. ...Tanaka, N. / Nakajima, M. / Narukawa-Nara, M. / Matsunaga, H. / Kamisuki, S. / Aramasa, H. / Takahashi, Y. / Sugimoto, N. / Abe, K. / Miyanaga, A. / Yamashita, T. / Sugawara, F. / Kamakura, T. / Komba, S. / Nakai, H. / Taguchi, H.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Identification, characterization, and structural analyses of a fungal endo-beta-1,2-glucanase reveal a new glycoside hydrolase family.
Authors: Tanaka, N. / Nakajima, M. / Narukawa-Nara, M. / Matsunaga, H. / Kamisuki, S. / Aramasa, H. / Takahashi, Y. / Sugimoto, N. / Abe, K. / Terada, T. / Miyanaga, A. / Yamashita, T. / Sugawara, F. ...Authors: Tanaka, N. / Nakajima, M. / Narukawa-Nara, M. / Matsunaga, H. / Kamisuki, S. / Aramasa, H. / Takahashi, Y. / Sugimoto, N. / Abe, K. / Terada, T. / Miyanaga, A. / Yamashita, T. / Sugawara, F. / Kamakura, T. / Komba, S. / Nakai, H. / Taguchi, H.
History
DepositionOct 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-1,2-glucanase
B: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,29913
Polymers113,2102
Non-polymers2,08911
Water5,224290
1
A: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2694
Polymers56,6051
Non-polymers6643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint11 kcal/mol
Surface area17730 Å2
MethodPISA
2
B: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0309
Polymers56,6051
Non-polymers1,4258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint15 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.657, 117.971, 93.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-876-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 25 - 516 / Label seq-ID: 13 - 504

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Sugars , 2 types, 9 molecules AB

#1: Protein Endo-beta-1,2-glucanase


Mass: 56604.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces funiculosus (fungus) / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H
References: UniProt: A0A4V8H012*PLUS, glucan endo-1,2-beta-glucosidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 294 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsThe authors submitted the sequence information to DDBJ and the accession number (LC430902) was assigned.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M citrate buffer (pH 4.1), 0.1M NaCl, 20%(w/v) PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.58 Å / Num. obs: 68894 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.174 / Num. unique obs: 4566 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
CRANK22.0.132phasing
XDSJune 1, 2017data reduction
Aimless0.7.3data scaling
BUCCANEER1.6.3model building
MOLREP7.0.060phasing
RefinementMethod to determine structure: SAD / Resolution: 2→46.58 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.727 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24807 3546 5.2 %RANDOM
Rwork0.21991 ---
obs0.22136 65277 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.006 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7807 0 134 290 8231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0148217
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177030
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.67211219
X-RAY DIFFRACTIONr_angle_other_deg0.8561.65616459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6585993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79723.735415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.265151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1851528
X-RAY DIFFRACTIONr_chiral_restr0.0540.21077
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021657
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8822.1183966
X-RAY DIFFRACTIONr_mcbond_other0.8822.1183965
X-RAY DIFFRACTIONr_mcangle_it1.3833.1744961
X-RAY DIFFRACTIONr_mcangle_other1.3833.1744962
X-RAY DIFFRACTIONr_scbond_it0.9932.2274251
X-RAY DIFFRACTIONr_scbond_other0.9932.2274251
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5633.3056259
X-RAY DIFFRACTIONr_long_range_B_refined2.36924.8329701
X-RAY DIFFRACTIONr_long_range_B_other2.33724.8089651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17638 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 286 -
Rwork0.269 4672 -
obs--99.58 %

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